Microwell plates (also known as microtiter plates) are often used in analytical research and clinical diagnostics. A microwell plate includes a plurality of sample wells (e.g., between 24 and 9,600 wells) containing liquid samples (e.g., incubated biological samples). Each sample well is analyzed by a plate reader system to detect specific biological events. However, prior systems and methods for analyzing the liquid samples in microwell plates suffer from tradeoffs between low-throughput multiplex analysis and high-throughput, non-multiplexed analysis. The present disclosure is directed to solving these and other problems.